| 2006 | 10 Years of the International Conference on Research in Computational Molecular Biology (RECOMB). Sarah J. Aerni, Eleazar Eskin |
| 2006 | A Branch-and-Reduce Algorithm for the Contact Map Overlap Problem. Wei Xie, Nikolaos V. Sahinidis |
| 2006 | A New Approach to Protein Identification. Nuno Bandeira, Dekel Tsur, Ari Frank, Pavel A. Pevzner |
| 2006 | A Novel Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles. Ivelin Georgiev, Ryan H. Lilien, Bruce Randall Donald |
| 2006 | A Parameterized Algorithm for Protein Structure Alignment. Jinbo Xu, Feng Jiao, Bonnie Berger |
| 2006 | A Parsimony Approach to Genome-Wide Ortholog Assignment. Zheng Fu, Xin Chen, Vladimir Vacic, Peng Nan, Yang Zhong, Tao Jiang |
| 2006 | A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies. Naftali Kaminski, Ziv Bar-Joseph |
| 2006 | A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer. Miklós Csürös, István Miklós |
| 2006 | A Study of Accessible Motifs and RNA Folding Complexity. Ydo Wexler, Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson |
| 2006 | A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds Metric. Nicholas D. Pattengale, Bernard M. E. Moret |
| 2006 | Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. Yun S. Song, Zhihong Ding, Dan Gusfield, Charles H. Langley, Yufeng Wu |
| 2006 | Alignment Statistics for Long-Range Correlated Genomic Sequences. Philipp W. Messer, Ralf Bundschuh, Martin Vingron, Peter F. Arndt |
| 2006 | An Important Connection Between Network Motifs and Parsimony Models. Teresa M. Przytycka |
| 2006 | An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets. Steffen Grossmann, Sebastian Bauer, Peter N. Robinson, Martin Vingron |
| 2006 | An Outsider's View of the Genome. Carl Zimmer |
| 2006 | Assessing Significance of Connectivity and Conservation in Protein Interaction Networks. Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski |
| 2006 | Biological Networks: Comparison, Conservation, and Evolutionary Trees. Benny Chor, Tamir Tuller |
| 2006 | CONTRAlign: Discriminative Training for Protein Sequence Alignment. Chuong B. Do, Samuel S. Gross, Serafim Batzoglou |
| 2006 | Clustering Near-Identical Sequences for Fast Homology Search. Michael Cameron, Yaniv Bernstein, Hugh E. Williams |
| 2006 | Clustering Short Gene Expression Profiles. Ling Wang, Marco Ramoni, Paola Sebastiani |
| 2006 | Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data. Jim C. Huang, Quaid Morris, Brendan J. Frey |
| 2006 | Detecting the Dependent Evolution of Biosequences. Jeremy Darot, Chen-Hsiang Yeang, David Haussler |
| 2006 | Efficient Enumeration of Phylogenetically Informative Substrings. Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim |
| 2006 | Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes. Kai Wang, Ilya Nemenman, Nilanjana Banerjee, Adam A. Margolin, Andrea Califano |
| 2006 | Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction. Brian Y. Chen, Viacheslav Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki |
| 2006 | Global Interaction Networks Probed by Mass Spectrometry. Anne-Claude Gavin |
| 2006 | Hypergraph Model of Multi-residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination. Xiaoduan Ye, Alan M. Friedman, Chris Bailey-Kellogg |
| 2006 | Improving Prediction of Zinc Binding Sites by Modeling the Linkage Between Residues Close in Sequence. Sauro Menchetti, Andrea Passerini, Paolo Frasconi, Claudia Andreini, Antonio Rosato |
| 2006 | Inferring Common Origins from mtDNA. Ajay K. Royyuru, Gabriela Alexe, Daniel E. Platt, Ravi Vijaya Satya, Laxmi Parida, Saharon Rosset, Gyan Bhanot |
| 2006 | Integrated Protein Interaction Networks for 11 Microbes. Balaji S. Srinivasan, Antal F. Novak, Jason Flannick, Serafim Batzoglou, Harley H. McAdams |
| 2006 | Leveraging Information Across HLA Alleles/Supertypes Improves Epitope Prediction. David Heckerman, Carl Myers Kadie, Jennifer Listgarten |
| 2006 | Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. Chakra Chennubhotla, Ivet Bahar |
| 2006 | Maximal Accurate Forests from Distance Matrices. Constantinos Daskalakis, Cameron Hill, Alexander Jaffe, Radu Mihaescu, Elchanan Mossel, Satish Rao |
| 2006 | Motif Yggdrasil: Sampling from a Tree Mixture Model. Samuel A. Andersson, Jens Lagergren |
| 2006 | New Methods for Detecting Lineage-Specific Selection. Adam C. Siepel, Katherine S. Pollard, David Haussler |
| 2006 | Permutation Filtering: A Novel Concept for Significance Analysis of Large-Scale Genomic Data. Stefanie Scheid, Rainer Spang |
| 2006 | Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. Sagi Snir, Lior Pachter |
| 2006 | Predicting Experimental Quantities in Protein Folding Kinetics Using Stochastic Roadmap Simulation. Tsung-Han Chiang, Mehmet Serkan Apaydin, Douglas L. Brutlag, David Hsu, Jean-Claude Latombe |
| 2006 | Protein Function Annotation Based on Ortholog Clusters Extracted from Incomplete Genomes Using Combinatorial Optimization. Akshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik |
| 2006 | RNA Secondary Structure Prediction Via Energy Density Minimization. Can Alkan, Emre Karakoç, Süleyman Cenk Sahinalp, Peter J. Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler |
| 2006 | Research in Computational Molecular Biology, 10th Annual International Conference, RECOMB 2006, Venice, Italy, April 2-5, 2006, Proceedings Alberto Apostolico, Concettina Guerra, Sorin Istrail, Pavel A. Pevzner, Michael S. Waterman |
| 2006 | Revealing the Proteome Complexity by Mass Spectrometry. Roman A. Zubarev |
| 2006 | Simple and Fast Inverse Alignment. John D. Kececioglu, Eagu Kim |
| 2006 | Simulating Protein Motions with Rigidity Analysis. Shawna L. Thomas, Xinyu Tang, Lydia Tapia, Nancy M. Amato |
| 2006 | Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions. Martin Bader, Enno Ohlebusch |
| 2006 | Stan Ulam and Computational Biology. Michael S. Waterman |
| 2006 | Statistical Evaluation of Genome Rearrangement. David Sankoff |
| 2006 | Structural Alignment of Pseudoknotted RNA. Banu Dost, Buhm Han, Shaojie Zhang, Vineet Bafna |
| 2006 | Ultraconserved Elements, Living Fossil Transposons, and Rapid Bursts of Change: Reconstructing the Uneven Evolutionary History of the Human Genome. David Haussler |